Difference between revisions of "GBrowseInstallation"

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(New page: Notes on installing Gbrowse in the WormBase environment. One barrier to packaging GBrowse with the rest of the wormbase code-base in CVS has been the architecture dependent paths that GB...)
 
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One barrier  to packaging GBrowse with the rest of the wormbase code-base in CVS has been the architecture dependent paths that GBrowse uses by default.  The following recipe gets rid of this "feature"
 
One barrier  to packaging GBrowse with the rest of the wormbase code-base in CVS has been the architecture dependent paths that GBrowse uses by default.  The following recipe gets rid of this "feature"
  
1) Check out a fresh copy of the 'stable' branch, or run 'make realclean' and do a CVS update.  If you have it, preserve the file GGB.def from the previous installation.
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1) Check out a fresh copy of the 'stable' branch, or run 'make realclean' and do a CVS update.  Create or edit the file GGB.def in the same directory as Makefile.PL.
  
 
'''GGB.def'''
 
'''GGB.def'''
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2) Run perl Makefile.PL with the usual options plus DO_XS=0.  You can either edit the GGB.def or use the command line args.  To contain the perl libraries, you can set the LIB option as well.  The DO_XS option is why the GBrowse libs have been going into architecture-dependent paths.  It concerns a tiny but rarely-used bit C code associated with one of the aligner plugins.  It is not used in the wormbase.
 
2) Run perl Makefile.PL with the usual options plus DO_XS=0.  You can either edit the GGB.def or use the command line args.  To contain the perl libraries, you can set the LIB option as well.  The DO_XS option is why the GBrowse libs have been going into architecture-dependent paths.  It concerns a tiny but rarely-used bit C code associated with one of the aligner plugins.  It is not used in the wormbase.
   perl Makefile.pl [ARGS]
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3) Do the installation with the incantation below. The UNINST=1 should remove the previous installation of libs in the architecture dependent paths but you will want to check to be sure.  Manually prune the directory  /system/dependent/path/Bio if necessary.  Check first to make sure bioperl is not installed in there (it should not be).
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   perl Makefile.pl
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3) Do the installation with the incantation below.  
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   sudo make install UNINST=1
 
   sudo make install UNINST=1
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4) The UNINST=1 should remove the previous installation of libs in the architecture dependent paths but you will want to check to be sure.  Manually prune the directory  /system/dependent/path/Bio if necessary.  Check first to make sure bioperl is not installed in there (it should not be).

Revision as of 07:45, 14 February 2008

Notes on installing Gbrowse in the WormBase environment.

One barrier to packaging GBrowse with the rest of the wormbase code-base in CVS has been the architecture dependent paths that GBrowse uses by default. The following recipe gets rid of this "feature"

1) Check out a fresh copy of the 'stable' branch, or run 'make realclean' and do a CVS update. Create or edit the file GGB.def in the same directory as Makefile.PL.

GGB.def

# This file is read by Makefile.PL

CGIBIN=/usr/local/wormbase/cgi-perl/seq
DO_XS=0
APACHE=/usr/local/apache
CONF=/usr/local/wormbase/conf
GBROWSE_ROOT=gbrowse
HTDOCS=/usr/local/wormbase/html
#LIB=/usr/local/wormbase/lib
VERSION=1.69
BIOGRAPHICS_VERSION=1.654

2) Run perl Makefile.PL with the usual options plus DO_XS=0. You can either edit the GGB.def or use the command line args. To contain the perl libraries, you can set the LIB option as well. The DO_XS option is why the GBrowse libs have been going into architecture-dependent paths. It concerns a tiny but rarely-used bit C code associated with one of the aligner plugins. It is not used in the wormbase.

 perl Makefile.pl

3) Do the installation with the incantation below.

 sudo make install UNINST=1

4) The UNINST=1 should remove the previous installation of libs in the architecture dependent paths but you will want to check to be sure. Manually prune the directory /system/dependent/path/Bio if necessary. Check first to make sure bioperl is not installed in there (it should not be).